Locus 2030

Sequence ID X_DroMel_CAF1
Location 5,583,698 – 5,583,857
Length 159
Max. P 0.771843
window3304 window3305

overview

Window 4

Location 5,583,698 – 5,583,817
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.88
Mean single sequence MFE -20.86
Consensus MFE -15.46
Energy contribution -15.90
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -1.56
Structure conservation index 0.74
SVM decision value 0.05
SVM RNA-class probability 0.557324
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5583698 119 - 22224390
CCCUCCACUC-CCCCUGCCCAUACAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUCGCUCCUCCAAAGCCUUUUACUUUUACCCAUUGCAUCAUUU
..........-....(((.........((((.(.((((((((((.....))))(...((.....))...))))))).).)))).....((((.......))))........)))...... ( -19.80)
>DroSec_CAF1 11826 106 - 1
CCCUCC-----CCC---CUCAUCAAAAAGCGUCGGCGACCAUGCCACAUGUAUGAAUGAUCCCUUCUCGCGGUCGCCGUCGCUCCUCCAAAACCUUU------AACCCAUUGCAUCAUUU
......-----...---..........((((.((((((((((((.....))))(...((.....))...))))))))).))))..............------................. ( -25.00)
>DroSim_CAF1 11951 106 - 1
CCCUCC-----CCC---CUCAUCAAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCCGUCACUCCUCCAAAACCUUU------AACCCAUUGCAUCAUUU
......-----...---..........((.(.((((((((((((.....))))(...((.....))...))))))))).).))..............------................. ( -19.60)
>DroEre_CAF1 12285 111 - 1
UUCUUAUAUG-CCCCUCCCGAUCCAAAGGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUU--CGCAGUCGCAGUCGCUCCUCCAAACCCUUU------UGCCCAUUGUAUCAUUU
..........-........(((.(((.((((.(.((((((((((.....)))))...((.....)--)...))))).).))))....((((....))------))....))).))).... ( -20.40)
>DroYak_CAF1 12344 114 - 1
CACCCACCUCCCCCCUCCCCAUCCAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUCGCUGCUCCAAAACCAUU------UACCCAUUUUAUUUUUU
...........................((((.(.((((((((((.....))))(...((.....))...))))))).).))))..............------................. ( -19.50)
>consensus
CCCUCC__U__CCCCU_CCCAUCCAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUCGCUCCUCCAAAACCUUU______UACCCAUUGCAUCAUUU
...........................((((.(.((((((((((.....))))(...((.....))...))))))).).))))..................................... (-15.46 = -15.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,583,738 – 5,583,857
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.11
Mean single sequence MFE -17.21
Consensus MFE -13.32
Energy contribution -13.72
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -0.56
Structure conservation index 0.77
SVM decision value 0.53
SVM RNA-class probability 0.771843
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5583738 119 - 22224390
AAAACCAUAUAUUUUCUCAUAAGGCAUACCCUUUCAGCUUCCCUCCACUC-CCCCUGCCCAUACAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUC
....................((((.....)))).................-...((((.((((((...((((.(....).))))....))))))...((((.(.....).)))))))).. ( -18.70)
>DroSec_CAF1 11860 104 - 1
AAAACCAUAUU--------UAAAGCAUACUCCUUUAGCACCCCUCC-----CCC---CUCAUCAAAAAGCGUCGGCGACCAUGCCACAUGUAUGAAUGAUCCCUUCUCGCGGUCGCCGUC
..........(--------(((((.......)))))).........-----...---.............(.((((((((((((.....))))(...((.....))...))))))))).) ( -18.30)
>DroSim_CAF1 11985 104 - 1
AAAUCCAUAUU--------UAAAGCAUACUCCUUUAGCACCCCUCC-----CCC---CUCAUCAAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCCGUC
..........(--------(((((.......)))))).........-----...---.............(.((((((((((((.....))))(...((.....))...))))))))).) ( -18.30)
>DroEre_CAF1 12319 95 - 1
-----UAUAUC--UCCUUUUAUCU---------------UUUCUUAUAUG-CCCCUCCCGAUCCAAAGGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUU--CGCAGUCGCAGUC
-----......--...........---------------........(((-((..............)))))..((((((((((.....)))))...((.....)--)...))))).... ( -14.84)
>DroYak_CAF1 12378 105 - 1
AUAAGCAUAUU--UUCUCAUAAGUCA-------------UCACCCACCUCCCCCCUCCCCAUCCAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUC
...........--.............-------------.............................(((.(.((((.(((((.....)))))...((.....)))))).).))).... ( -15.90)
>consensus
AAAACCAUAUU__U_CU__UAAAGCAUAC_C_UU_AGC_UCCCUCC__U__CCCCU_CCCAUCCAAAAGCGUCGGCGACCAUGCCCCAUGUAUGAAUGAUCCCUUCUCGCGGUCGCAGUC
....................................................................(((.(.((((.(((((.....)))))...((.....)))))).).))).... (-13.32 = -13.72 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:36 2006